HEADER TRANSFERASE 18-MAR-05 1Z5M TITLE CRYSTAL STRUCTURE OF N1-[3-[[5-BROMO-2-[[3-[(1-PYRROLIDINYLCARBONYL) TITLE 2 AMINO]PHENYL]AMINO]-4-PYRIMIDINYL]AMINO]PROPYL]-2,2- TITLE 3 DIMETHYLPROPANEDIAMIDE COMPLEXED WITH HUMAN PDK1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN; COMPND 5 SYNONYM: HPDK1; COMPND 6 EC: 2.7.1.37; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PDPK1, PDK1; SOURCE 6 EXPRESSION_SYSTEM: UNIDENTIFIED BACULOVIRUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10469; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF-21 CELLS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PBLUEBAC4.5; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDK1-CAT-PBB4.5 KEYWDS PROTEIN INHIBITOR COMPLEX, SERINE KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.WHITLOW,M.ADLER REVDAT 6 23-AUG-23 1Z5M 1 REMARK SEQADV LINK REVDAT 5 11-OCT-17 1Z5M 1 REMARK REVDAT 4 13-JUL-11 1Z5M 1 VERSN REVDAT 3 24-FEB-09 1Z5M 1 VERSN REVDAT 2 07-JUN-05 1Z5M 1 JRNL REVDAT 1 19-APR-05 1Z5M 0 JRNL AUTH R.I.FELDMAN,J.M.WU,M.A.POLOKOFF,M.J.KOCHANNY,H.DINTER,D.ZHU, JRNL AUTH 2 S.L.BIROC,B.ALICKE,J.BRYANT,S.YUAN,B.O.BUCKMAN,D.LENTZ, JRNL AUTH 3 M.FERRER,M.WHITLOW,M.ADLER,S.FINSTER,Z.CHANG,D.O.ARNAIZ JRNL TITL NOVEL SMALL MOLECULE INHIBITORS OF JRNL TITL 2 3-PHOSPHOINOSITIDE-DEPENDENT KINASE-1. JRNL REF J.BIOL.CHEM. V. 280 19867 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15772071 JRNL DOI 10.1074/JBC.M501367200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.M.BIONDI,D.KOMANDER,C.C.THOMAS,J.M.LIZCANO,M.DEAK, REMARK 1 AUTH 2 D.R.ALESSI,D.M.F.VAN AALTEN REMARK 1 TITL HIGH RESOLUTION CRYSTAL STRUCTURE OF THE HUMAN PDK1 REMARK 1 TITL 2 CATALYTIC DOMAIN DEFINES THE REGULATORY PHOSPHOPEPTIDE REMARK 1 TITL 3 DOCKING SITE REMARK 1 REF EMBO J. V. 21 4219 2002 REMARK 1 REFN ISSN 0261-4189 REMARK 1 PMID 12169624 REMARK 1 DOI 10.1093/EMBOJ/CDF437 REMARK 2 REMARK 2 RESOLUTION. 2.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 21580 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 915 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.17 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.27 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 85 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2255 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.18000 REMARK 3 B22 (A**2) : 1.18000 REMARK 3 B33 (A**2) : -2.35000 REMARK 3 B12 (A**2) : 1.61000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.770 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.460 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Z5M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 94.2 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1. REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(220); REMARK 200 CYLINDRICALLY BENT REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21597 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.170 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.417 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08740 REMARK 200 FOR THE DATA SET : 8.3300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.77 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34700 REMARK 200 FOR SHELL : 2.140 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDK1 HOMOLOGY MODEL BUILT FROM PDB ENTRY 1O6L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS, EDTA, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.31333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.65667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 15.65667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.31333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 231 REMARK 465 PRO A 232 REMARK 465 GLU A 233 REMARK 465 SER A 234 REMARK 465 LYS A 235 REMARK 465 GLN A 236 REMARK 465 ALA A 237 REMARK 465 ARG A 238 REMARK 465 ALA A 239 REMARK 465 ASN A 240 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 151 -166.85 -115.06 REMARK 500 ASP A 205 39.49 -156.30 REMARK 500 ASP A 223 70.40 70.10 REMARK 500 THR A 255 -94.68 -117.63 REMARK 500 LYS A 257 18.18 45.23 REMARK 500 GLU A 343 -50.19 -28.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 333 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 THE INHIBITION CONSTANT (KI APPARENT) REMARK 600 FOR N-(3-{[5-BROMO-2-({3-[(PYRROLIDIN-1- REMARK 600 YLCARBONYL)AMINO]PHENYL}AMINO)PYRIMIDIN REMARK 600 -4-YL]AMINO}PROPYL)-2,2-DIMETHYLMALONAMIDE REMARK 600 AGAINST PDK1 WAS MEASURED AS 30 NM (N=5) REMARK 600 DIRECT MEASURE PDK1 ACTIVITY WAS PERFORMED REMARK 600 BY THE FOLLOWING PROTOCOL: THE FINAL REMARK 600 ASSAY MIXTURE (60 UL) CONTAINED 50 MM TRIS- REMARK 600 HCL, PH 7.5, 0.1 MM EGTA, 0.1 MM EDTA, 0.1% REMARK 600 BETA-MERCAPTOETHANOL, 1 MG/ML BOVINE SERUM REMARK 600 ALBUMIN, 10 MM MGOAC, 10 UM ATP, 0.2 UCI OF REMARK 600 [GAMMA-33P]ATP, 7.5 UM OF SUBSTRATE PEPTIDE REMARK 600 (H2NARRRGVTTKTFCGT) AND 60 NG OF PURIFIED REMARK 600 RECOMBINANT HUMAN PDK1. AFTER 4 H AT ROOM REMARK 600 TEMPERATURE, WE ADDED 25 MM EDTA AND SPOTTED A REMARK 600 PORTION OF THE REACTION MIXTURE ON WHATMAN P81 REMARK 600 PHOSPHOCELLULOSE PAPER. THE FILTER PAPER WAS REMARK 600 WASHED 3 TIMES WITH 0.75% PHOSPHORIC ACID AND REMARK 600 ONCE WITH ACETONE. AFTER DRYING, THE FILTER-BOUND REMARK 600 LABELED PEPTIDE WAS QUANTIFIED USING A FUJI REMARK 600 PHOSPHOIMAGER. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 698 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LI8 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 607 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UU7 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH BIM-2 REMARK 900 RELATED ID: 1UU8 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH BIM-1 REMARK 900 RELATED ID: 1UU9 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH BIM-3 REMARK 900 RELATED ID: 1UVR RELATED DB: PDB REMARK 900 SAME PROTEIN WITH BIM-8 REMARK 900 RELATED ID: 1H1W RELATED DB: PDB REMARK 900 SAME PROTEIN WITH ATP DBREF 1Z5M A 74 359 UNP O15530 PDPK1_HUMAN 74 359 SEQADV 1Z5M SEP A 241 UNP O15530 SER 241 MODIFIED RESIDUE SEQRES 1 A 286 PRO ARG LYS LYS ARG PRO GLU ASP PHE LYS PHE GLY LYS SEQRES 2 A 286 ILE LEU GLY GLU GLY SER PHE SER THR VAL VAL LEU ALA SEQRES 3 A 286 ARG GLU LEU ALA THR SER ARG GLU TYR ALA ILE LYS ILE SEQRES 4 A 286 LEU GLU LYS ARG HIS ILE ILE LYS GLU ASN LYS VAL PRO SEQRES 5 A 286 TYR VAL THR ARG GLU ARG ASP VAL MET SER ARG LEU ASP SEQRES 6 A 286 HIS PRO PHE PHE VAL LYS LEU TYR PHE THR PHE GLN ASP SEQRES 7 A 286 ASP GLU LYS LEU TYR PHE GLY LEU SER TYR ALA LYS ASN SEQRES 8 A 286 GLY GLU LEU LEU LYS TYR ILE ARG LYS ILE GLY SER PHE SEQRES 9 A 286 ASP GLU THR CYS THR ARG PHE TYR THR ALA GLU ILE VAL SEQRES 10 A 286 SER ALA LEU GLU TYR LEU HIS GLY LYS GLY ILE ILE HIS SEQRES 11 A 286 ARG ASP LEU LYS PRO GLU ASN ILE LEU LEU ASN GLU ASP SEQRES 12 A 286 MET HIS ILE GLN ILE THR ASP PHE GLY THR ALA LYS VAL SEQRES 13 A 286 LEU SER PRO GLU SER LYS GLN ALA ARG ALA ASN SEP PHE SEQRES 14 A 286 VAL GLY THR ALA GLN TYR VAL SER PRO GLU LEU LEU THR SEQRES 15 A 286 GLU LYS SER ALA CYS LYS SER SER ASP LEU TRP ALA LEU SEQRES 16 A 286 GLY CYS ILE ILE TYR GLN LEU VAL ALA GLY LEU PRO PRO SEQRES 17 A 286 PHE ARG ALA GLY ASN GLU TYR LEU ILE PHE GLN LYS ILE SEQRES 18 A 286 ILE LYS LEU GLU TYR ASP PHE PRO GLU LYS PHE PHE PRO SEQRES 19 A 286 LYS ALA ARG ASP LEU VAL GLU LYS LEU LEU VAL LEU ASP SEQRES 20 A 286 ALA THR LYS ARG LEU GLY CYS GLU GLU MET GLU GLY TYR SEQRES 21 A 286 GLY PRO LEU LYS ALA HIS PRO PHE PHE GLU SER VAL THR SEQRES 22 A 286 TRP GLU ASN LEU HIS GLN GLN THR PRO PRO LYS LEU THR MODRES 1Z5M SEP A 241 SER PHOSPHOSERINE HET SEP A 241 10 HET SO4 A 600 5 HET CL A 698 1 HET LI8 A 501 35 HET GOL A 602 6 HET GOL A 606 6 HET GOL A 607 6 HETNAM SEP PHOSPHOSERINE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM LI8 N-(3-{[5-BROMO-2-({3-[(PYRROLIDIN-1-YLCARBONYL) HETNAM 2 LI8 AMINO]PHENYL}AMINO)PYRIMIDIN-4-YL]AMINO}PROPYL)-2,2- HETNAM 3 LI8 DIMETHYLMALONAMIDE HETNAM GOL GLYCEROL HETSYN SEP PHOSPHONOSERINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 SO4 O4 S 2- FORMUL 3 CL CL 1- FORMUL 4 LI8 C23 H31 BR N8 O3 FORMUL 5 GOL 3(C3 H8 O3) FORMUL 8 HOH *74(H2 O) HELIX 1 1 ARG A 78 GLU A 80 5 3 HELIX 2 2 LYS A 115 GLU A 121 1 7 HELIX 3 3 LYS A 123 LEU A 137 1 15 HELIX 4 4 GLU A 166 GLY A 175 1 10 HELIX 5 5 ASP A 178 LYS A 199 1 22 HELIX 6 6 THR A 245 VAL A 249 5 5 HELIX 7 7 SER A 250 THR A 255 1 6 HELIX 8 8 CYS A 260 GLY A 278 1 19 HELIX 9 9 ASN A 286 LEU A 297 1 12 HELIX 10 10 PHE A 306 GLU A 314 1 9 HELIX 11 11 ASP A 320 ARG A 324 5 5 HELIX 12 12 CYS A 327 GLU A 331 5 5 HELIX 13 13 GLY A 332 ALA A 338 1 7 HELIX 14 14 HIS A 339 GLU A 343 5 5 HELIX 15 15 THR A 346 GLN A 353 5 8 SHEET 1 A 5 PHE A 82 GLU A 90 0 SHEET 2 A 5 THR A 95 GLU A 101 -1 O LEU A 98 N GLY A 85 SHEET 3 A 5 GLU A 107 GLU A 114 -1 O ILE A 110 N VAL A 97 SHEET 4 A 5 LYS A 154 LEU A 159 -1 O LEU A 155 N LEU A 113 SHEET 5 A 5 LEU A 145 GLN A 150 -1 N TYR A 146 O GLY A 158 SHEET 1 B 2 ILE A 201 ILE A 202 0 SHEET 2 B 2 LYS A 228 VAL A 229 -1 O LYS A 228 N ILE A 202 SHEET 1 C 2 ILE A 211 LEU A 213 0 SHEET 2 C 2 ILE A 219 ILE A 221 -1 O GLN A 220 N LEU A 212 LINK C SEP A 241 N PHE A 242 1555 1555 1.33 SITE 1 AC1 4 LYS A 76 THR A 148 PHE A 149 GLN A 150 SITE 1 AC2 3 LYS A 111 THR A 222 LI8 A 501 SITE 1 AC3 18 LEU A 88 GLY A 89 GLU A 90 GLY A 91 SITE 2 AC3 18 SER A 94 VAL A 96 ALA A 109 LYS A 111 SITE 3 AC3 18 LEU A 159 SER A 160 TYR A 161 ALA A 162 SITE 4 AC3 18 LYS A 163 GLY A 165 GLU A 166 LEU A 212 SITE 5 AC3 18 ASP A 223 CL A 698 SITE 1 AC4 7 PHE A 82 LYS A 83 PHE A 84 GLU A 194 SITE 2 AC4 7 GLY A 334 LYS A 337 HOH A 731 SITE 1 AC5 5 PHE A 84 LYS A 154 TYR A 156 GLU A 331 SITE 2 AC5 5 HOH A 731 SITE 1 AC6 4 LEU A 113 TYR A 126 GLU A 130 GLY A 225 CRYST1 124.610 124.610 46.970 90.00 90.00 120.00 P 32 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008025 0.004633 0.000000 0.00000 SCALE2 0.000000 0.009267 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021290 0.00000